Gustavo Seabra писал 07.02.2020 19:02:
> Hi,
> This structure has at least 2 residues (LYZ and HYP) that are not
> present
> in the AMBER force field templates. Before trying to load it, you must
> prepare parameters for them. I'd recommend you take a look into the
> AMBER
> Tutorials here (http://ambermd.org/tutorials/), and especially the ones
> in
> this list: http://ambermd.org/tutorials/ForceField.php.
>
> All the best,
> --
> Gustavo Seabra.
>
>
> On Fri, Feb 7, 2020 at 9:10 AM Johannes Kalliauer <
> johannes.kalliauer.tuwien.ac.at> wrote:
>
>> Dear AmberUsers!
>>
>> I get the error
>>
>> > FATAL: Atom .R<LYZ 0000>.A<CA 1> does not have a type.
>> in leap.
>>
>> I read
>> - http://archive.ambermd.org/201212/0122.html
>> - http://archive.ambermd.org/201006/0253.html
>> -
>>
>> https://www.researchgate.net/post/How_to_solve_Amber_Leap_PDB_preparation_error_atom_does_not_have_a_type
>>
>> but the problem persist, and I still don't understand how I can
>> resolve
>> the problem.
>>
>> How to reproduce the error:
>>
>> > #!/bin/bash
>> >
>> > #download PDB-file from https://www.rcsb.org/structure/3HR2
>> > wget -O 3hr2.pdb https://files.rcsb.org/download/3hr2.pdb
>> >
>> > tleap -f ./Input.leap
>> >
>> with input.leap:
>> > source leaprc.protein.ff14SB
>> > source leaprc.water.tip3p
>> > source leaprc.lipid17
>> > source leaprc.gaff2
>> > source leaprc.DNA.bsc1
>> > source leaprc.DNA.OL15
>> > source leaprc.protein.ff14SB
>> >
>> > COL1A1= loadpdb "3hr2.pdb"
>> > saveamberparm COL1A1 COL1A1.prmtop COL1A1.inpcrd
>> >
>> I get following error-messages:
>> > FATAL: Atom .R<LYZ 103>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 700>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 934>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 946>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1150>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1171>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1237>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1282>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1327>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1711>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 1987>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 2183>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 2780>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 3014>.A<CA 1> does not have a type.
>> > FATAL: Atom .R<LYZ 3026>.A<CA 1> does not have a type.
>> >
>> > /home/jkalliau/prgm/amber18/bin/teLeap: Fatal Error!
>> > Failed to generate parameters
>>
>> Hope for an answer, best Regards
>> Johannes Kalliauer
>> TU-Wien (Vienna)
>>
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Received on Fri Feb 07 2020 - 09:00:02 PST
